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genome_info.txt file not created by build_midas_db.py #60

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snayfach opened this issue Jun 3, 2017 · 0 comments
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genome_info.txt file not created by build_midas_db.py #60

snayfach opened this issue Jun 3, 2017 · 0 comments

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@snayfach
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snayfach commented Jun 3, 2017

Causes the following error when running merge_midas.py snps:

Traceback (most recent call last):
  File "/global/projectb/scratch/snayfach/tools/MIDAS-dev/scripts/merge_midas.py", line 441, in <module>
    run_program(program, args)
  File "/global/projectb/scratch/snayfach/tools/MIDAS-dev/scripts/merge_midas.py", line 431, in run_program
    snps.run_pipeline(args)
  File "/global/projectb/scratch/snayfach/tools/MIDAS-dev/midas/merge/snps.py", line 382, in run_pipeline
    species_list = merge.select_species(args, dtype='snps')
  File "/global/projectb/scratch/snayfach/tools/MIDAS-dev/midas/merge/merge.py", line 161, in select_species
    species = init_species(samples, args, dtype)
  File "/global/projectb/scratch/snayfach/tools/MIDAS-dev/midas/merge/merge.py", line 130, in init_species
    genome_info = read_genome_info(args['db'])
  File "/global/projectb/scratch/snayfach/tools/MIDAS-dev/midas/merge/merge.py", line 100, in read_genome_info
    for r in csv.DictReader(open(path), delimiter='\t'):
IOError: [Errno 2] No such file or directory: '/global/projectb/scratch/snayfach/projects/dc4/midas_db/genome_info.txt'
snayfach pushed a commit that referenced this issue Jun 6, 2017
Improvements to db building code
647a719 
-<genome>.features no longer required input file; file built automatically by identifying genomic locations of <genome>.ffn
-replaced usearch with vsearch
-added function to write genome_info.txt file; addresses issue #60
@snayfach snayfach closed this as completed Jun 6, 2017
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